A computer program allows the separation of a wide range of chromosome sizes by pulsed field gel electrophoresis

DNA damage-inducible and RAD52-independent repair of DNA double-strand breaks in Saccharomyces cerevisiae

Chromosomal repair was studied in stationary-phase Saccharomyces cerevisiae, including rad52/rad52 mutant strains deficient in repairing double-strand breaks (DSBs) by homologous recombination. Mutant strains suffered more chromosomal fragmentation than RAD52/RAD52 strains after treatments with cobalt-60 gamma irradiation or radiomimetic bleomycin, except after high bleomycin doses when chromosomes from rad52/rad52 strains contained fewer DSBs than chromosomes from RAD52/RAD52 strains. DNAs from both genotypes exhibited quick rejoining following gamma irradiation and sedimentation in isokinetic alkaline sucrose gradients, but only chromosomes from RAD52/RAD52 strains exhibited slower rejoining (10 min to 4 hr in growth medium). Chromosomal DSBs introduced by gamma irradiation and bleomycin were analyzed after pulsed-field gel electrophoresis. After equitoxic damage by both DNA-damaging agents, chromosomes in rad52/rad52 cells were reconstructed under nongrowth conditions [liquid holding (LH)]. Up to 100% of DSBs were eliminated and survival increased in RAD52/RAD52 and rad52/rad52 strains. After low doses, chromosomes were sometimes degraded and reconstructed during LH. Chromosomal reconstruction in rad52/rad52 strains was dose dependent after gamma irradiation, but greater after high, rather than low, bleomycin doses with or without LH. These results suggest that a threshold of DSBs is the requisite signal for DNA-damage-inducible repair, and that nonhomologous end-joining repair or another repair function is a dominant mechanism in S. cerevisiae when homologous recombination is impaired.

Physical map of the chromosome of the phytopathogenic bacterium Pseudomonas syringae pv. phaseolicola

Pseudomonas syringae pv. phaseolicola (P.s. phaseolicola) is one of about 45 recognized pathovars within the P. syringae group and is the causal agent of halo-blight disease of beans. DNA from this bacterium digested to completion with two different restriction enzymes, PacI and PmeI, yielded 15 and 16 fragments, respectively. These were separated using PFGE and sized by comparison to known molecular mass markers. The P.s. phaseolicola chromosome was determined to be approximately 5.64 Mb in size. To link the different fragments obtained into a circular chromosome map for both enzymes, 150 random Tn5 mutants of P.s. phaseolicola were used as a source of DNA and the identification of the band carrying the transposon ‘tag’ in each mutant was done after PFGE and Southern hybridization of a complete chromosomal digestion using a Tn5 probe. Partial digestions of DNA from different Tn5 mutants ‘tagging’ specific bands were then generated and the complete and partial products of the digestion separated by PFGE and identified with a Tn5 probe. By calculating the size of the partial products, it was then possible to link different bands into a physical map. This is the first report on the construction of a physical map of a member of the P. syringae group and should be invaluable for molecular genetic analysis in this species and in evolutionary or taxonomic studies when compared to similar data obtained for any of the other recognized pathovars.

An electrophoretic approach to the assessment of the spatial distribution of DNA double-strand breaks in mammalian cells

An approach is presented making it possible to investigate whether breaks in fragmented mammalian chromosomal DNA were induced randomly and independently from each other. Genomic DNA isolated from mammalian cells irradiated with gamma-rays or restriction enzyme-treated human DNA was resolved according to size using pulsed field gel electrophoresis, and the resulting DNA mass distributions were measured in ethidium bromide-stained gels. The DNA profiles thus obtained were compared to the predictions on DNA fragment size distribution which follow from a so-called random breakage model to test whether the experimental outcome is compatible with the assumption of a random localization of breaks. Comparisons of fragment distributions may be performed utilizing two equivalent representations that are linked by an adequate transformation. Considering either directly measurable DNA mass profiles in units of migration distances along a gel lane or transformed distributions in units of molecular length, we show for gamma-irradiated samples that the predictions derived from the employed models agree well with the observed data, thus allowing an immediate quantification of double-strand breaks (DSB). Using restriction enzyme-treated DNA as a paradigm, the disagreement of predicted and observed data shows the applicability of our approach to the detection of a non-random distribution of DSB. Therefore, we suppose that our approach may also be useful to reveal a clustering of DSB, which is postulated to occur after damage induction by densely ionizing radiation. Furthermore, investigations on the spatial distribution of chemically or endogenously produced DSB, as well as residual DSB after repair, may be attempted.

Pulsed-field gel electrophoresis analysis of the repair of psoralen plus UVA induced DNA photoadducts in Saccharomyces cerevisiae

In the yeast Saccharomyces cerevisiae, double-strand breaks (DSB) have been observed during the DNA repair of psoralen plus UVA induced lesions. In the present paper, we analyzed this repair step in some detail using pulsed-field gel electrophoresis (CHEF) to get a better understanding of this phenomenon with regard to the type of lesions induced and the repair pathways involved. The results confirm that, during post-treatment incubation of Saccharomyces cerevisiae cells, DSB are formed. Their appearance is dose-dependent and the rate of induction is comparable in large (chromosome IV) and small (chromosome III) chromosomes. The formation of DSB is evidenced by the breakage of linear chromosomes III and IV, but also, after high doses, by the linearization of a circular form of chromosome III. The induction of DSB appears to be highly dependent on the induction of interstrand cross-links since they are clearly present after treatments with 8-MOP plus 365 nm radiation (inducing monoadducts and cross-linking in DNA), but practically absent after treatment with 8-MOP plus 405 nm radiation (inducing predominantly monoadducts) at comparable levels of photoadducts. The occurrence of DSB is dependent on the RAD2 and RAD52, but not on the RAD6 gene. It is likely that the specific processing of DNA lesions involving DSB is related to the genotoxic consequences observed.

Repair of DNA double-strand breaks induced in Saccharomyces cerevisiae using different gamma-ray dose-rates: a pulsed-field gel electrophoresis analysis

We investigated the effects of gamma-ray exposures at high dose-rate (HDR, 23.2 Gy/min) and low dose-rate (LDR, 0.47 Gy/min) on survival and the induction of DNA double-strand breaks (dsb) in a diploid wild-type (D7) and the repair-deficient mutant strain rad52/rad52 of Saccharomyces cerevisiae. Analysis by pulsed-field gel electrophoresis (PFGE) using a contour homogeneous electric field apparatus revealed that, at HDR, in the range 0-400 Gy, dsb are induced as a linear function of gamma-ray dose. Liquid holding recovery in non-nutrient medium (LHR) for 48 h of wild-type cells treated at HDR, significantly increased survival and reduced the yield of dsb. Such changes did not occur in rad52/rad52 cells defective in the repair of dsb. Thus, in gamma-irradiated wild-type cells, an efficient repair of dsb is taking place during LHR. Treatments of wild-type cells at LDR resulted in higher survival and an approximately two-fold lower yield of dsb than at HDR. Such a dose-rate effect was absent in rad52/rad52 cells suggesting that, in wild-type cells during LDR exposures, significant amounts of dsb can be repaired. This repair could be very much accentuated by 48-h LHR of wild-type cells treated at LDR. The relationship observed between gamma-ray survival and dsb repair clearly indicates that increases in survival of wild-type cells, during LDR as compared with HDR exposures and after LHR, are strongly related to the repair of dsb.

DNA sequence analysis of the YCN2 region of chromosome XI in Saccharomyces cerevisiae

A 6.8 kbp DNA fragment localized to the left arm of chromosome XI from Saccharomyces cerevisiae was sequenced and analysed (EMBL accession no. X69765). Two genes involved in protein phosphatase activity were identified: YCN2 and an open reading frame encoding a protein that shares 46% amino acid identity with the sds22+ protein from Schizosaccharomyces pombe. A comparison of the genomic YCN2 sequence with the published cDNA sequence suggests the presence of an intron near the 5' end of the gene. Further sequence analysis suggests the presence of three additional genes near YCN2: a mitochondrial acyl-carrier protein, a gene encoding a putative hydrophobic protein, and a new gene coding for a tRNA(Leu) (UAA) isoacceptor located near a delta sequence.

Analysis of the MSS51 region on chromosome XII of Saccharomyces cerevisiae

We have localized gene MSS51 on chromosome XII of Saccharomyces cerevisiae between the RDN1 and CDC42 loci. 'Head to head' with MSS51 is another gene, QRI5, the function of which is unknown. However, the proximity of these genes, the structure of the intergenic region and the presence of an ABF1 binding site right in the middle of this region suggest that the MSS51 and QRI5 expressions are submitted to a common regulatory process.

An angle-variable three-dimensional pulsed field gel electrophoresis system

A three-dimensional pulsed field electrophoretic method based on the simultaneous application of fixed and cyclically alternating polarity fields at a right angle is described. Requiring only minimal electronic hardware it provides highly homogeneous field conditions over a large gel area and the versatility to vary the pulse vector angle. The electrophoretic parameters critical to achieve fast high resolution separation over a wide range of molecular sizes have been optimized and applied to megabase-size chromosomal DNA molecules. The empirical relationships between pulse time, field strength conditions, and resolution limits derived allow selection of coordinated experimental conditions for the separation of specific DNA size ranges.

Semiconductor-controlled contour-clamped homogeneous electric field apparatus

The design and construction of a transistor-driven hexagonal contour-clamped homogeneous electric field (CHEF) apparatus is discussed in detail. The addition of computer control of pulsed-field timings and experiment duration gives rise to an efficient electrophoresis tool designed to achieve separation of DNA molecules in different size groupings. In particular, pulse time regimes which lead to the monotonic separation of DNA molecules ranging from 90 kbp to over a megabase pair are demonstrated. Theoretical treatment of electric field clamping with transistor-driven multiple electrodes is supported by measurements and by the actual performance of electrophoretic separation of yeast chromosomes. The large sample capacity of gels run in this apparatus coupled with the modest power requirements necessary to provide a homogeneous electric field offer significant advantages over earlier CHEF designs.

Field inversion gel electrophoresis with different pulse time ramps

The influence of different pulse time ramps on the separation of yeast chromosomes with field inversion gel electrophoresis (FIGE) was investigated by the means of two dimensional gel electrophoresis. The problem of band inversion, which makes it difficult to distinguish DNA molecules of different size, has been solved by using double randomized pulse times. A major disadvantage of the field inversion technique is thereby overcome, making this system comparable to other pulsed field techniques.

Determination of genome size of Pseudomonas aeruginosa by PFGE: analysis of restriction fragments

Genomic DNA size was measured in three strains of Pseudomonas aeruginosa, ATCC 29260 (exotoxin A), ATCC 33467 (type I smooth) and ATCC 33468 (type 2 mucoid) by transverse alternating field electrophoresis of restriction fragments. Because of the high (67%) G + C content of Pseudomonas aeruginosa, restriction enzymes that recognize sequences with at least 4 AT base pairs were expected to be rare cutters. Eight enzymes produced fragments greater than 200 kb in size: Dral (TTT/AAA), Asnl (ATT/AAT), Hpal (GTT/AAC), AfIII (C/TTAAG), Xbal (T/CTAGA), Spel (A/CTAGT), Sspl (AAT/ATT) and Ndel (CA/TATG). All eight enzymes recognized one of three rare tetranucleotide sequences, TTAA, CTAG or ATAT. Pseudomonas aeruginosa strain 29260 has a genomic DNA size of 5573 kb. Strains 33467 and 33468 have identical restriction patterns and a possible deletion with a genomic size of 5407 kb.

Repair of furocoumarin-plus-UVA-induced damage and mutagenic consequences in eukaryotic cells

In the presence of near-UV radiation (UVA) furocoumarins (psoralens) photoinduce defined lesions in DNA, i.e. monoadducts and interstrand crosslinks. Their use in photochemotherapy (psoralen plus UVA (PUVA) treatment) and cosmetics raises questions concerning the repairability of these lesions and their genotoxic consequences. We have analysed the repair of psoralen photoadducts in cultured eukaryotic cells, such as yeast and mammalian cells, for furocoumarins of photochemotherapeutic interest. In yeast, the interaction of repair pathways differs in exogenous (plasmid) and endogenous (chromosomal) DNA. The order of mutagenic activity is 4,5',8-trimethylpsoralen greater than 5-methoxypsoralen greater than 8-methoxypsoralen greater than 7-methylpyrido[3,4-c]psoralen greater than 3-carbethoxypsoralen. The mutagenicity is dependent on psoralen functionality, concentration and bioavailability, maximal UVA dose, wavelength, dose (fluence) rate and presence or absence of chemical filters. It probably involves an inducible component. Chromosome breakage occurs during the repair period after PUVA treatment. It appears that the genotoxic effects of psoralens are produced by a specific arrangement of induced photolesions and the interaction of different repair systems.

The alcohol dehydrogenase system in the yeast, Kluyveromyces lactis

We have studied the alcohol dehydrogenase (ADH) system in the yeast Kluyveromyces lactis. Southern hybridization to the Saccharomyces cerevisiae ADH2 gene indicates four probable structural ADH genes in K. lactis. Two of these genes have been isolated from a genomic bank by hybridization to ADH2. The nucleotide sequence of one of these genes shows 80% and 50% sequence identity to the ADH genes of S. cerevisiae and Schizosaccharomyces pombe respectively. One K. lactis ADH gene is preferentially expressed in glucose-grown cells and, in analogy to S. cerevisiae, was named K1ADH1. The other gene, homologous to K1ADH1 in sequence, shows an amino-terminal extension which displays all of the characteristics of a mitochondrial targeting presequence. We named this gene K1ADH3. The two genes have been localized on different chromosomes by Southern hybridization to an orthogonal-field-alternation gel electrophoresis-resolved K. lactis genome. ADH activities resolved by gel electrophoresis revealed several ADH isozymes which are differently expressed in K. lactis cells depending on the carbon source.

Control of pulsed field gel electrophoresis at short switching intervals by a microcomputer

Pulsed field gel electrophoresis allows not only the separation of very large DNA molecules (up to 10 megabase pairs) but also gives an enhanced resolution in separations of DNA in the size range of 10-100 kilobase pairs (kbp). For this application, rapid alternation of the electrical field polarity is required. Here we describe equipment for the delivery of short switching pulses that is easy and inexpensive to build and is controlled by a standard microcomputer. It has proved to be useful in the separation of lambda DNA and its fragments. Parameters for enhanced separation of 23- and 48-kbp DNA molecules at high voltage gradients (15 V/cm) are presented and shown to provide superior resolution when compared to those for conventional electrophoresis at both high and low voltage gradients.

A physical map around the WAGR complex on the short arm of chromosome 11

A long-range restriction map of part of the short arm of chromosome 11 including the WAGR region has been constructed using pulsed-field gel electrophoresis and a number of infrequently cutting restriction enzymes. A total of 15.4 Mbp has been mapped in detail, extending from proximal 11p14 to the distal part of 11p12. The map localizes 35 different DNA probes and reveals at least nine areas with features characteristic of HTF islands, some of which may be candidates for the different loci underlying the phenotype of the WAGR syndrome. This map will furthermore allow screening of DNA from individuals with WAGR-related phenotypes and from Wilms tumors for associated chromosomal rearrangements.

Effect of nonparallel alternating fields on the mobility of DNA in the biased reptation model of gel electrophoresis

Chromosome-size DNA molecules can now be separated using a variety of pulsed field gel electrophoresis techniques. In this article, we study the predictions of the biased reptation model concerning the effect of two pulsed fields, making an arbitrary angle, on the power of separation of gel electrophoresis. Separation is predicted to be largely enhanced for obtuse angles, in agreement with experiments. Interestingly, very large molecules, which are not separated by pulsed fields, are predicted not to migrate along the gel diagonal for fairly long periods of time. Finally, we discuss the optimization of these techniques using the results of the theory, and the limitations of the latter when fluctuations and intramolecular modes probably dominate the system.

Analysis of chromosomal DNA patterns of the genus Kluyveromyces

Using an improved procedure of pulsed field gel electrophoresis, yeast chromosomes were separated over a wide range of molecular size (250-4000 kbp) on single gels. The chromosomal DNA patterns of all the species belonging to the genus Kluyveromyces were examined. Within the species K. marxianus, the varieties lactis, drosophilarum and vanudenii showed closely related patterns: very different from them, the varieties bulgaricus and marxianus were related to each other, forming a distinct group; the strains commonly called 'K. lactis' and 'K. fragilis' were unambiguously different from each other in chromosome patterns. These differences were correlated with the presence of characteristic repetitive sequence elements in the mitochondrial DNA of the former group and not in the latter. Analysis of Candida macedoniensis, which had been considered to be an anamorph of K. marxianus var. marxianus, showed that these two yeast species were indeed similar in chromosome patterns and in mitochondrial DNA restriction patterns.